In Orchidaceae, many species are subjected to decline due to direct or indirect human activities. Within terrestrial species, genus Epipactis provides a suitable model to analyze its susceptibility to environmental changes. It consists of several groups of close species, varying in reproductive patterns and growing in various ecological conditions. It is not particularly threatened by plant or flower collection. Data from large participative orchid inventory in France can be used to detect range migration. Phylogeny studies allowed identification of various clades but relationships and gene flow among taxa remain unclear. Few data on their genome organization are available. Genome size reveals variation among taxa without clear relationships to published phylogenies. It is not more related to the allogamy to autogamy switch. Stomatal guard cell size is partly related to genome size. Hybrids can be observed even between species from separated clades, revealing a low differentiation. Controlled interspecific hybridization leads to normal seeds. Seed germination and protocorm development remains erratic in natural conditions which limit comparison of different seed types in spite of seeds produced by controlled crossing between plants growing in different stands seems to grow better than selfing or crosses among plants of the same stands in allogamous species. In vitro germination of mature seeds did not provide the expected success. Non-mature seeds are thus tested. Such possible inbreeding address question on population genetic structure and differentiation. The development of new molecular markers for diversity assessment is done from RNAseq (14 106 reads in total) of flowers studies in order to reduce the sequencing effort due to the large genome size of the genus (2C: 25-30 pg DNA). Polymorphic sites (5% of showed variation including indels) are observed in expressed sequences by sequencing from different plants. Flower expressed genes consist of various gene classes with a large amount (> 30 %) related to transposable elements.